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Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing.

dc.contributor.author Rothfels, CJ
dc.contributor.author Pryer, KM
dc.contributor.author Li, F
dc.date.accessioned 2020-11-30T15:08:06Z
dc.date.available 2020-11-30T15:08:06Z
dc.date.issued 2017-01
dc.identifier.issn 1469-8137
dc.identifier.issn 1469-8137
dc.identifier.uri https://hdl.handle.net/10161/21753
dc.description.abstract Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (Pipeline for Untangling Reticulate Complexes (Purc)) that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multi-labeled species tree for a subset of our accessions. We amplified four c. 1-kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. Purc infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads, Purc was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and, in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
dc.language eng
dc.publisher Wiley
dc.relation.ispartof The New phytologist
dc.relation.isversionof 10.1111/nph.14111
dc.subject Sequence Analysis, DNA
dc.subject Hybridization, Genetic
dc.subject Computational Biology
dc.subject Phylogeny
dc.subject Recombination, Genetic
dc.subject Base Sequence
dc.subject Consensus Sequence
dc.subject Polyploidy
dc.subject Alleles
dc.subject Databases, Genetic
dc.subject Biological Evolution
dc.title Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing.
dc.type Journal article
duke.contributor.id Pryer, KM|0079353
dc.date.updated 2020-11-30T15:08:05Z
pubs.begin-page 413
pubs.end-page 429
pubs.issue 1
pubs.organisational-group Trinity College of Arts & Sciences
pubs.organisational-group Biology
pubs.organisational-group Duke Science & Society
pubs.organisational-group Duke
pubs.organisational-group Initiatives
pubs.organisational-group Institutes and Provost's Academic Units
pubs.publication-status Published
pubs.volume 213
duke.contributor.orcid Pryer, KM|0000-0002-9776-6736


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